Most Intra-Galactic Warp gates paralyze units that travel through it for 1 minute in friendly territory and 2 minutes in neutral or hostile territory.
The Mercenaries and Advanced Production gates paralyze units that travel through it for 4 seconds in friendly territory and 8 seconds in neutral or hostile territory.
The Fabricators gate does not paralyze units that travel through it.

How to use in your fleet

The Intra-Galactic Warp Gate is useful for allowing you to deploy newly constructed units near or on the frontlines. This is very useful if you're production buildings are located a very long ways away from where you need your ships to be.